In Mystery of the Abbey, each player plays the role of a monk seeking to solve a murder in an abbey along the lines of The Name of the Rose. The game is similar to Cluedo in that the objective is to identify a murderer by process of elimination by moving from room to room in a monastery and asking questions of other players in order to force them to reveal information that will disqualify potential suspects.

Unlike Cluedo, a player, on his turn, can ask any question to any player provided the response would not include a suspect's name. The person being asked the question may choose to answer or otherwise refuse by putting a finger to his lips (i.e. taking a vow of silence). If the player does elect to answer the question, he then has the right to immediately ask his own question to the first player.

Players use the suspects' characteristics to help identify the murderer. The 24 suspects are differentiated by their association with one of three monastic orders (Franciscan, Benedictine and Templar), their title (Father, Brother and Novice), whether they are wearing a hood, whether they have a beard, and whether they are fat or thin.

Game rules, special cards and other elements are designed around the theme of the monastery and monastic life. Although most of these can directly impact the outcome of the game, some are intended to simply add an element of fun and atmosphere (for example, one card calls for all questions in the next round to be asked in Gregorian chant).